Since its original development in the early 1980s,[2] the USGS have released four major releases, and is now considered to be the de facto standard code for aquifer simulation. There are several actively developed commercial and non-commercial graphical user interfaces for MODFLOW.

The water must have a constant density, dynamic viscosity (and consequently temperature) throughout the modelling domain (SEAWAT is a modified version of MODFLOW which is designed for density-dependent groundwater flow and transport)

The principal components of anisotropy of the hydraulic conductivity used in MODFLOW is displayed on the right. This tensor does not allow non-orthogonal anisotropies, as could be expected from flow in fractures. Horizontal anisotropy for an entire layer can be represented by the coefficient "TRPY" (Data Item 3 Page 153.[3]

The USGS throughout the 1970s had developed several hundred models, written in different dialects of FORTRAN. At the time, it was common practice to rewrite a new model to fit the need of a new groundwater scenario. The concept for MODFLOW was originally designed in 1981 to provide a common modular groundwater model, which could be compiled on multiple platforms without major (or any) modification, and can read and write common formats. Different aspects of the groundwater system would be handled using the modules, similar to the idea of a "component stereo system". The original name of the code was "The USGS Modular Three-Dimensional Finite-Difference Ground-Water Flow Model", or informally as "The Modular Model." The name MODFLOW was coined several years after the initial code development, which started in 1981.[2]

The first version of MODFLOW[3] was published on December 28, 1983, and was coded entirely in FORTRAN 66. The source code for this version is listed in USGS Open File Report 83-875 referred to above.

This version of MODFLOW[4] was rewritten in FORTRAN 77, and was originally released on July 24, 1987. The current version of MODFLOW-88 is 2.6, released on September 20, 1996.

MODPATH, was initially developed in 1989 to post-process the steady-state MODFLOW-88 data to determine three-dimensional pathlines of particles. This innovation has been indispensable for the fields of contaminanthydrogeology. It is still used as a post-processor in recent versions of MODFLOW.

A separate program, MODFLOWP, was developed in 1992 to estimate various parameters used in MODFLOW. This program was eventually built into MODFLOW-2000.

MODFLOW-2000 (version 1.0; version numbering was reset) was released on July 20, 2000, which merged MODFLOWP and HYDMOD codes into the main program.[7] Many new packages and enhancements were also included, including new solvers, stream and saturated flow packages. The internal design concepts also changed from previous versions, such that packages, processes and modules are distinct. This version was coded in a mixture of FORTRAN 77, Fortran 90, and C. MODFLOW-2000 can also be compiled for parallel computing, which can allow multiple processors to be used to increase model complexity and/or reduce simulation time.

The final version of MODFLOW-2000 (or MF2K) is version 1.19.01, released on March 25, 2010. There are four related or branched codes based on MODFLOW-2000:

This is the current version of MODFLOW.[8] It is written primarily in Fortran 90 and C.

The current version of MODFLOW-2005 is version 1.11.00, released on August 8, 2013. Related or branched codes include:

MODFLOW-OWHM[9] (version 1.00.00, September 15, 2014), The One-Water Hydrologic Flow Model (MODFLOW-OWHM, MF-OWHM or MODFLOW-ONE[10]), is a fusion of multiple versions of MODFLOW (NWT, LGR, FMP, SWR, SWI) into ONE version, contains upgrades and new features and allows the simulation of head-dependent flows, flow-dependent flows, and deformation dependent flows that collectively affect conjunctive use of water resources and provides an online input guide

MODFLOW-USG[11] was initially released in 2013, which is designed to adapted to a wide range of grid variations using unstructured grids. The current version of MODFLOW-USG is version 1.2.00, released 21 March 2014.

Non-commercial MODFLOW versions are free, however, their licensing usually limit the use to non-profit educational or research purposes.

ModelMuse is a grid-independent graphical user interface from the USGS for MODFLOW-2005, MODPATH, and PHAST. There are no license restrictions. The source code is included.

MODFLOW-GUI – Made by the USGS: it is updated often to match the current USGS MODFLOW development. It supports MODFLOW-96, MODFLOW-2000, MODFLOW-2005, MODPATH, ZONEBUDGET, GWT, MT3DMS, SEAWAT, and GWM. Source code for MODFLOW-GUI is included. It depends on Argus ONE: a commercial interface for constructing generic models. There are no license restrictions beyond those of Argus ONE.

PMWIN – "Processing MODFLOW" (for Windows) – powerful freeware for MODFLOW processing and visualization, provided alongside an instructional book;[13] also available in Traditional Chinese. The license for this version is limited to non-commercial use.

mflab - mflab is a MATLAB interface to MODFLOW. The user builds and analyzes models by writing a set of MATLAB scripts. This results in flexible and efficient workflows, allowing a great deal of automation.

Commercial MODFLOW programs are typically used by governments and consultants for practical applications of MODFLOW to real-world groundwater problems. Professional versions of MODFLOW are generally priced at a minimum of around $1000 and typically range upward to $7000 USD. This is a list of commercial programs for MODFLOW: